Starting phenix.real_space_refine on Mon Sep 14 17:37:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbm_13295/09_2026/7pbm_13295_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbm_13295/09_2026/7pbm_13295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pbm_13295/09_2026/7pbm_13295_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbm_13295/09_2026/7pbm_13295_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pbm_13295/09_2026/7pbm_13295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbm_13295/09_2026/7pbm_13295.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 45 5.49 5 Mg 3 5.21 5 S 101 5.16 5 C 10134 2.51 5 N 2757 2.21 5 O 3220 1.98 5 H 15819 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32079 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "B" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 4895 Classifications: {'peptide': 309} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4934 Classifications: {'peptide': 313} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "E" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "F" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 719 Classifications: {'peptide': 48} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 760 Classifications: {'peptide': 50} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "U" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 480 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "V" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 474 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.35, per 1000 atoms: 0.17 Number of scatterers: 32079 At special positions: 0 Unit cell: (125.35, 137.34, 107.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 101 16.00 P 45 15.00 Mg 3 11.99 O 3220 8.00 N 2757 7.00 C 10134 6.00 H 15819 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 874.6 milliseconds 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 20 sheets defined 59.1% alpha, 10.9% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.554A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.606A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 100 removed outlier: 3.542A pdb=" N LEU A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.925A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.806A pdb=" N MET A 163 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.670A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 211 Processing helix chain 'A' and resid 216 through 234 removed outlier: 3.551A pdb=" N GLN A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 251 removed outlier: 3.868A pdb=" N ASP A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 removed outlier: 3.610A pdb=" N GLY A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 290 through 297 removed outlier: 3.626A pdb=" N GLU A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.782A pdb=" N LEU A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 removed outlier: 3.637A pdb=" N MET A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 48 removed outlier: 3.568A pdb=" N ILE B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.671A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 90 through 98 removed outlier: 3.564A pdb=" N LEU B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 116 through 130 removed outlier: 4.916A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 216 through 234 Processing helix chain 'B' and resid 240 through 251 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.799A pdb=" N ASN B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.624A pdb=" N LEU B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 removed outlier: 3.525A pdb=" N HIS B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 28 Processing helix chain 'C' and resid 31 through 49 Processing helix chain 'C' and resid 64 through 77 removed outlier: 3.753A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.584A pdb=" N LEU C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 116 through 130 removed outlier: 3.575A pdb=" N GLU C 121 " --> pdb=" O MET C 117 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU C 128 " --> pdb=" O TYR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 165 through 170 removed outlier: 3.534A pdb=" N ALA C 170 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.590A pdb=" N GLU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 212 removed outlier: 3.581A pdb=" N LEU C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 234 removed outlier: 3.531A pdb=" N TYR C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 252 removed outlier: 3.657A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 273 removed outlier: 3.554A pdb=" N LEU C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 290 through 298 removed outlier: 3.504A pdb=" N GLU C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.860A pdb=" N LEU C 302 " --> pdb=" O TYR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.532A pdb=" N TYR D 28 " --> pdb=" O PHE D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.727A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 77 Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.729A pdb=" N LEU D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU D 101 " --> pdb=" O ILE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 115 Processing helix chain 'D' and resid 116 through 129 removed outlier: 4.673A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 142 Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 182 through 194 removed outlier: 4.457A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 211 Processing helix chain 'D' and resid 216 through 232 removed outlier: 3.525A pdb=" N ARG D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 251 removed outlier: 3.515A pdb=" N GLN D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 273 Processing helix chain 'D' and resid 279 through 288 removed outlier: 3.687A pdb=" N ASN D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.576A pdb=" N LEU D 302 " --> pdb=" O TYR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 Processing helix chain 'E' and resid 31 through 48 removed outlier: 3.627A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.643A pdb=" N PHE E 70 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 90 through 100 removed outlier: 3.683A pdb=" N LEU E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 130 removed outlier: 3.614A pdb=" N GLU E 120 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.501A pdb=" N ILE E 196 " --> pdb=" O ARG E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 213 removed outlier: 3.769A pdb=" N LEU E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 234 removed outlier: 3.927A pdb=" N ASP E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 251 removed outlier: 3.596A pdb=" N GLN E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 279 through 287 Processing helix chain 'E' and resid 290 through 298 removed outlier: 3.622A pdb=" N ASP E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 305 removed outlier: 3.557A pdb=" N LEU E 302 " --> pdb=" O TYR E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.504A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 47 " --> pdb=" O GLU F 43 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 77 removed outlier: 3.593A pdb=" N PHE F 70 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 90 through 99 removed outlier: 3.784A pdb=" N LEU F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'F' and resid 116 through 130 removed outlier: 4.529A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU F 128 " --> pdb=" O TYR F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 142 Processing helix chain 'F' and resid 165 through 170 removed outlier: 3.557A pdb=" N ALA F 170 " --> pdb=" O ASN F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 197 Processing helix chain 'F' and resid 202 through 212 Processing helix chain 'F' and resid 216 through 234 removed outlier: 4.084A pdb=" N ASP F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 251 Processing helix chain 'F' and resid 259 through 273 removed outlier: 3.891A pdb=" N GLU F 271 " --> pdb=" O ARG F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 288 Processing helix chain 'F' and resid 290 through 298 Processing helix chain 'F' and resid 298 through 305 Processing helix chain 'F' and resid 318 through 326 removed outlier: 3.638A pdb=" N TYR F 322 " --> pdb=" O THR F 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 170 Processing helix chain 'G' and resid 173 through 183 Processing helix chain 'G' and resid 190 through 202 Processing helix chain 'H' and resid 159 through 170 Processing helix chain 'H' and resid 173 through 184 removed outlier: 3.700A pdb=" N ILE H 184 " --> pdb=" O MET H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 199 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 3.548A pdb=" N ASP A 110 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU A 107 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ALA A 157 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 109 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 136 removed outlier: 3.506A pdb=" N ILE A 136 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 200 through 201 removed outlier: 7.146A pdb=" N THR A 200 " --> pdb=" O ILE A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 84 removed outlier: 6.442A pdb=" N LYS B 81 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASP B 110 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR B 83 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU B 107 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA B 157 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE B 109 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 136 Processing sheet with id=AA7, first strand: chain 'B' and resid 308 through 311 Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 84 removed outlier: 3.515A pdb=" N ASP C 110 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 107 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ALA C 157 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE C 109 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C 56 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 136 Processing sheet with id=AB1, first strand: chain 'C' and resid 308 through 311 Processing sheet with id=AB2, first strand: chain 'D' and resid 80 through 84 removed outlier: 6.244A pdb=" N LEU D 107 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA D 157 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE D 109 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR D 55 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N THR D 158 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU D 57 " --> pdb=" O THR D 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 131 through 136 Processing sheet with id=AB4, first strand: chain 'D' and resid 308 through 311 Processing sheet with id=AB5, first strand: chain 'E' and resid 80 through 84 removed outlier: 6.559A pdb=" N LYS E 81 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ASP E 110 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR E 83 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU E 107 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ALA E 157 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE E 109 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU E 56 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 131 through 136 Processing sheet with id=AB7, first strand: chain 'E' and resid 200 through 201 removed outlier: 7.056A pdb=" N THR E 200 " --> pdb=" O ILE E 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 308 through 311 Processing sheet with id=AB9, first strand: chain 'F' and resid 80 through 84 removed outlier: 6.401A pdb=" N LEU F 107 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ALA F 157 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE F 109 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 131 through 136 removed outlier: 3.521A pdb=" N ILE F 134 " --> pdb=" O VAL F 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 308 through 311 766 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 7.23 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 15819 1.06 - 1.28: 2721 1.28 - 1.50: 6908 1.50 - 1.72: 6779 1.72 - 1.94: 199 Bond restraints: 32426 Sorted by residual: bond pdb=" N THR F 19 " pdb=" H1 THR F 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR E 19 " pdb=" H1 THR E 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR D 19 " pdb=" H1 THR D 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N SER G 156 " pdb=" H1 SER G 156 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N THR A 19 " pdb=" H1 THR A 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 32421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 57979 2.04 - 4.08: 620 4.08 - 6.13: 66 6.13 - 8.17: 13 8.17 - 10.21: 14 Bond angle restraints: 58692 Sorted by residual: angle pdb=" O4' DA V 11 " pdb=" C1' DA V 11 " pdb=" N9 DA V 11 " ideal model delta sigma weight residual 108.00 111.07 -3.07 7.00e-01 2.04e+00 1.92e+01 angle pdb=" N PHE B 197 " pdb=" CA PHE B 197 " pdb=" C PHE B 197 " ideal model delta sigma weight residual 110.41 105.10 5.31 1.23e+00 6.61e-01 1.86e+01 angle pdb=" N3 DT U 7 " pdb=" C4 DT U 7 " pdb=" O4 DT U 7 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT V 3 " pdb=" C4 DT V 3 " pdb=" O4 DT V 3 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT V 4 " pdb=" C4 DT V 4 " pdb=" O4 DT V 4 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.62e+01 ... (remaining 58687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.07: 14461 32.07 - 64.14: 582 64.14 - 96.21: 45 96.21 - 128.28: 1 128.28 - 160.35: 5 Dihedral angle restraints: 15094 sinusoidal: 8661 harmonic: 6433 Sorted by residual: dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 100.36 -160.35 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O2A ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PA ADP D 600 " pdb=" PB ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 86.89 -146.89 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" O1B ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PB ADP D 600 " pdb=" PA ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 76.64 -136.65 1 2.00e+01 2.50e-03 4.15e+01 ... (remaining 15091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2296 0.079 - 0.157: 240 0.157 - 0.236: 8 0.236 - 0.315: 3 0.315 - 0.393: 1 Chirality restraints: 2548 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.73 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C3' AGS B 401 " pdb=" C2' AGS B 401 " pdb=" C4' AGS B 401 " pdb=" O3' AGS B 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C3' AGS A 401 " pdb=" C2' AGS A 401 " pdb=" C4' AGS A 401 " pdb=" O3' AGS A 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 2545 not shown) Planarity restraints: 4702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 192 " -0.156 9.50e-02 1.11e+02 7.14e-02 5.63e+01 pdb=" NE ARG C 192 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG C 192 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 192 " -0.057 2.00e-02 2.50e+03 pdb=" NH2 ARG C 192 " 0.082 2.00e-02 2.50e+03 pdb="HH11 ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 192 " 0.067 2.00e-02 2.50e+03 pdb="HH21 ARG C 192 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG C 192 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 312 " -0.445 9.50e-02 1.11e+02 1.53e-01 5.48e+01 pdb=" NE ARG F 312 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG F 312 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG F 312 " 0.052 2.00e-02 2.50e+03 pdb=" NH2 ARG F 312 " 0.062 2.00e-02 2.50e+03 pdb="HH11 ARG F 312 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG F 312 " -0.037 2.00e-02 2.50e+03 pdb="HH21 ARG F 312 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG F 312 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 31 " 0.044 2.00e-02 2.50e+03 5.51e-02 4.55e+01 pdb=" CD GLN C 31 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLN C 31 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN C 31 " -0.088 2.00e-02 2.50e+03 pdb="HE21 GLN C 31 " -0.003 2.00e-02 2.50e+03 pdb="HE22 GLN C 31 " 0.085 2.00e-02 2.50e+03 ... (remaining 4699 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1058 2.17 - 2.78: 60711 2.78 - 3.39: 82482 3.39 - 3.99: 107541 3.99 - 4.60: 172414 Nonbonded interactions: 424206 Sorted by model distance: nonbonded pdb="HH21 ARG E 312 " pdb=" OP1 DA V 10 " model vdw 1.564 2.450 nonbonded pdb=" OE2 GLU C 128 " pdb="HH22 ARG D 218 " model vdw 1.570 2.450 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.570 2.450 nonbonded pdb=" HH TYR A 273 " pdb=" OD1 ASN A 286 " model vdw 1.591 2.450 nonbonded pdb=" O ALA F 138 " pdb=" HG1 THR F 141 " model vdw 1.593 2.450 ... (remaining 424201 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'B' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'C' and resid 19 through 330) selection = (chain 'D' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'E' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'F' and (resid 19 through 136 or resid 141 through 330)) } ncs_group { reference = (chain 'G' and (resid 158 through 202 or (resid 203 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name H or name H \ A or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or n \ ame HD21 or name HD22 or name HD23)))) selection = (chain 'H' and resid 158 through 203) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.440 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 16607 Z= 0.255 Angle : 0.783 10.210 22614 Z= 0.454 Chirality : 0.047 0.393 2548 Planarity : 0.011 0.154 2808 Dihedral : 15.620 160.355 6466 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.06 % Allowed : 1.28 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.18), residues: 1950 helix: -1.47 (0.14), residues: 1035 sheet: 0.35 (0.30), residues: 298 loop : 0.22 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG C 114 TYR 0.033 0.005 TYR F 131 PHE 0.019 0.003 PHE F 25 HIS 0.011 0.003 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.25 (16607) covalent geometry : angle 0.78347 / 0.45 (22614) hydrogen bonds : bond 0.26593 / 17.87 ( 793) hydrogen bonds : angle 8.53690 / 5.93 ( 2241) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 427 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.9007 (mmm) cc_final: 0.8648 (mmt) REVERT: A 79 ASN cc_start: 0.7865 (m-40) cc_final: 0.7274 (m-40) REVERT: A 110 ASP cc_start: 0.8071 (t0) cc_final: 0.7844 (t70) REVERT: A 178 MET cc_start: 0.9017 (mmm) cc_final: 0.8766 (mmt) REVERT: A 222 ARG cc_start: 0.7838 (ttp-170) cc_final: 0.7478 (ttm170) REVERT: A 309 MET cc_start: 0.7229 (ttm) cc_final: 0.7017 (ttp) REVERT: C 121 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7608 (mt-10) REVERT: C 144 SER cc_start: 0.6230 (p) cc_final: 0.5753 (p) REVERT: C 178 MET cc_start: 0.9112 (mmt) cc_final: 0.8637 (mmt) REVERT: C 234 MET cc_start: 0.8723 (mmt) cc_final: 0.8435 (mmt) REVERT: C 325 MET cc_start: 0.9365 (mmm) cc_final: 0.9162 (mmp) REVERT: D 105 ASP cc_start: 0.7600 (m-30) cc_final: 0.7169 (m-30) REVERT: E 105 ASP cc_start: 0.6662 (m-30) cc_final: 0.6107 (m-30) REVERT: E 330 THR cc_start: 0.7829 (m) cc_final: 0.7548 (p) REVERT: F 102 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7400 (mm-30) REVERT: F 298 TYR cc_start: 0.7431 (m-80) cc_final: 0.7200 (m-80) REVERT: H 200 ARG cc_start: 0.7827 (ttt180) cc_final: 0.7509 (mmm-85) outliers start: 1 outliers final: 1 residues processed: 428 average time/residue: 0.3393 time to fit residues: 204.2408 Evaluate side-chains 263 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 286 ASN E 304 GLN G 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.127314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.099904 restraints weight = 66814.798| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.25 r_work: 0.2926 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16607 Z= 0.186 Angle : 0.672 6.735 22614 Z= 0.367 Chirality : 0.044 0.174 2548 Planarity : 0.006 0.051 2808 Dihedral : 15.208 168.558 2653 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.79 % Allowed : 6.34 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.18), residues: 1950 helix: -0.16 (0.15), residues: 1062 sheet: 0.46 (0.31), residues: 277 loop : 0.20 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 48 TYR 0.027 0.001 TYR C 124 PHE 0.010 0.001 PHE D 70 HIS 0.007 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (16607) covalent geometry : angle 0.67203 / 0.37 (22614) hydrogen bonds : bond 0.07879 / 5.26 ( 793) hydrogen bonds : angle 5.86659 / 4.11 ( 2241) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 276 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.9186 (tpp) cc_final: 0.8817 (tpp) REVERT: A 76 MET cc_start: 0.8997 (mmm) cc_final: 0.8721 (mmt) REVERT: A 79 ASN cc_start: 0.8410 (m-40) cc_final: 0.7835 (m-40) REVERT: A 178 MET cc_start: 0.9234 (mmm) cc_final: 0.9025 (mmt) REVERT: A 199 MET cc_start: 0.7856 (mmt) cc_final: 0.7586 (mmt) REVERT: A 222 ARG cc_start: 0.8190 (ttp-170) cc_final: 0.7787 (ttm170) REVERT: A 309 MET cc_start: 0.8175 (ttm) cc_final: 0.7884 (ttp) REVERT: C 110 ASP cc_start: 0.8737 (t0) cc_final: 0.8475 (m-30) REVERT: C 121 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7905 (mt-10) REVERT: C 147 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7307 (mp) REVERT: C 178 MET cc_start: 0.9235 (mmt) cc_final: 0.8730 (mmt) REVERT: E 81 LYS cc_start: 0.8367 (mttt) cc_final: 0.7653 (tptt) REVERT: E 105 ASP cc_start: 0.7996 (m-30) cc_final: 0.7683 (m-30) REVERT: E 127 MET cc_start: 0.8076 (mtp) cc_final: 0.7726 (mtm) REVERT: E 272 MET cc_start: 0.8172 (mtt) cc_final: 0.7911 (mtt) REVERT: E 325 MET cc_start: 0.7159 (mmm) cc_final: 0.6901 (mmp) REVERT: E 330 THR cc_start: 0.7860 (m) cc_final: 0.7548 (p) REVERT: F 234 MET cc_start: 0.7751 (ttm) cc_final: 0.7528 (ttm) REVERT: F 240 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7323 (t70) REVERT: F 252 ASP cc_start: 0.7969 (m-30) cc_final: 0.7352 (p0) REVERT: H 200 ARG cc_start: 0.8111 (ttt180) cc_final: 0.7607 (mtp-110) outliers start: 13 outliers final: 8 residues processed: 284 average time/residue: 0.3251 time to fit residues: 131.6135 Evaluate side-chains 255 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 245 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain H residue 199 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 107 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 103 optimal weight: 0.2980 chunk 181 optimal weight: 0.0040 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.128297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.100936 restraints weight = 66404.430| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.24 r_work: 0.3013 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 16607 Z= 0.143 Angle : 0.567 6.559 22614 Z= 0.303 Chirality : 0.041 0.321 2548 Planarity : 0.005 0.053 2808 Dihedral : 14.742 171.186 2653 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.04 % Allowed : 7.25 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.19), residues: 1950 helix: 0.32 (0.16), residues: 1069 sheet: 0.14 (0.31), residues: 257 loop : 0.25 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 179 TYR 0.021 0.001 TYR C 124 PHE 0.007 0.001 PHE C 197 HIS 0.008 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (16607) covalent geometry : angle 0.56717 / 0.30 (22614) hydrogen bonds : bond 0.06278 / 4.21 ( 793) hydrogen bonds : angle 5.27702 / 3.70 ( 2241) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 261 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7730 (mt-10) REVERT: A 76 MET cc_start: 0.8987 (mmm) cc_final: 0.8778 (mmt) REVERT: A 79 ASN cc_start: 0.8393 (m-40) cc_final: 0.7831 (m-40) REVERT: A 178 MET cc_start: 0.9233 (mmm) cc_final: 0.8990 (mmt) REVERT: A 222 ARG cc_start: 0.8244 (ttp-170) cc_final: 0.7897 (ttm170) REVERT: A 309 MET cc_start: 0.8173 (ttm) cc_final: 0.7916 (ttp) REVERT: C 110 ASP cc_start: 0.8633 (t0) cc_final: 0.8399 (m-30) REVERT: C 121 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7818 (mt-10) REVERT: C 147 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7492 (mp) REVERT: C 178 MET cc_start: 0.9276 (mmt) cc_final: 0.8872 (mmt) REVERT: E 81 LYS cc_start: 0.8416 (mttt) cc_final: 0.7774 (tptt) REVERT: E 272 MET cc_start: 0.8036 (mtt) cc_final: 0.7821 (mtt) REVERT: E 325 MET cc_start: 0.7320 (mmm) cc_final: 0.7104 (mmp) REVERT: E 328 ASP cc_start: 0.7924 (t0) cc_final: 0.7615 (m-30) REVERT: E 330 THR cc_start: 0.7995 (m) cc_final: 0.7693 (p) REVERT: F 84 SER cc_start: 0.8810 (p) cc_final: 0.8599 (t) REVERT: F 100 ASP cc_start: 0.8184 (t0) cc_final: 0.7978 (t0) REVERT: H 200 ARG cc_start: 0.8093 (ttt180) cc_final: 0.7590 (mtp-110) outliers start: 17 outliers final: 12 residues processed: 269 average time/residue: 0.3278 time to fit residues: 126.0681 Evaluate side-chains 253 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 240 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 199 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 125 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.125373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.097834 restraints weight = 66745.093| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.24 r_work: 0.2981 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16607 Z= 0.222 Angle : 0.606 6.124 22614 Z= 0.322 Chirality : 0.042 0.140 2548 Planarity : 0.005 0.048 2808 Dihedral : 14.644 166.339 2653 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.28 % Allowed : 7.68 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.19), residues: 1950 helix: 0.37 (0.16), residues: 1065 sheet: -0.06 (0.31), residues: 253 loop : -0.10 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 143 TYR 0.025 0.001 TYR C 124 PHE 0.011 0.001 PHE C 152 HIS 0.012 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (16607) covalent geometry : angle 0.60556 / 0.32 (22614) hydrogen bonds : bond 0.06153 / 4.08 ( 793) hydrogen bonds : angle 5.08427 / 3.57 ( 2241) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 253 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8954 (mmm) cc_final: 0.8721 (mmt) REVERT: A 79 ASN cc_start: 0.8391 (m-40) cc_final: 0.7836 (m-40) REVERT: A 222 ARG cc_start: 0.8284 (ttp-170) cc_final: 0.7910 (ttm170) REVERT: A 309 MET cc_start: 0.8260 (ttm) cc_final: 0.7986 (ttp) REVERT: C 110 ASP cc_start: 0.8702 (t0) cc_final: 0.8464 (m-30) REVERT: C 121 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7898 (mt-10) REVERT: C 147 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7508 (mp) REVERT: C 178 MET cc_start: 0.9291 (mmt) cc_final: 0.8805 (mmt) REVERT: E 81 LYS cc_start: 0.8520 (mttt) cc_final: 0.7787 (tptt) REVERT: E 272 MET cc_start: 0.8090 (mtt) cc_final: 0.7854 (mtt) REVERT: E 330 THR cc_start: 0.8139 (m) cc_final: 0.7824 (p) REVERT: F 252 ASP cc_start: 0.8035 (m-30) cc_final: 0.7338 (p0) REVERT: F 296 ASP cc_start: 0.7615 (m-30) cc_final: 0.7336 (m-30) REVERT: H 200 ARG cc_start: 0.8150 (ttt180) cc_final: 0.7637 (mtp-110) outliers start: 21 outliers final: 17 residues processed: 262 average time/residue: 0.3224 time to fit residues: 121.0457 Evaluate side-chains 260 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 242 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 199 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 161 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.098032 restraints weight = 67196.284| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.17 r_work: 0.3001 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16607 Z= 0.133 Angle : 0.539 6.225 22614 Z= 0.285 Chirality : 0.040 0.134 2548 Planarity : 0.005 0.065 2808 Dihedral : 14.489 167.861 2653 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.04 % Allowed : 8.53 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 1950 helix: 0.58 (0.16), residues: 1069 sheet: 0.23 (0.30), residues: 281 loop : 0.08 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 160 TYR 0.019 0.001 TYR C 124 PHE 0.007 0.001 PHE A 58 HIS 0.007 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (16607) covalent geometry : angle 0.53870 / 0.28 (22614) hydrogen bonds : bond 0.05278 / 3.51 ( 793) hydrogen bonds : angle 4.87807 / 3.42 ( 2241) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 249 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8937 (mmm) cc_final: 0.8736 (mmt) REVERT: A 79 ASN cc_start: 0.8334 (m-40) cc_final: 0.7773 (m-40) REVERT: A 222 ARG cc_start: 0.8283 (ttp-170) cc_final: 0.7946 (ttm170) REVERT: A 286 ASN cc_start: 0.7806 (OUTLIER) cc_final: 0.7472 (m110) REVERT: A 309 MET cc_start: 0.8177 (ttm) cc_final: 0.7918 (ttp) REVERT: C 110 ASP cc_start: 0.8643 (t0) cc_final: 0.8391 (m-30) REVERT: C 147 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7517 (mp) REVERT: C 178 MET cc_start: 0.9243 (mmt) cc_final: 0.8728 (mmt) REVERT: E 81 LYS cc_start: 0.8489 (mttt) cc_final: 0.7780 (tptt) REVERT: E 272 MET cc_start: 0.8079 (mtt) cc_final: 0.7854 (mtt) REVERT: E 328 ASP cc_start: 0.7948 (t0) cc_final: 0.7710 (m-30) REVERT: E 330 THR cc_start: 0.8118 (m) cc_final: 0.7812 (p) REVERT: F 252 ASP cc_start: 0.7921 (m-30) cc_final: 0.7281 (p0) REVERT: H 200 ARG cc_start: 0.8157 (ttt180) cc_final: 0.7659 (mtp-110) outliers start: 17 outliers final: 10 residues processed: 255 average time/residue: 0.3222 time to fit residues: 117.4058 Evaluate side-chains 251 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 239 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 4 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.098170 restraints weight = 66894.124| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.17 r_work: 0.2990 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16607 Z= 0.161 Angle : 0.545 6.276 22614 Z= 0.286 Chirality : 0.041 0.132 2548 Planarity : 0.005 0.045 2808 Dihedral : 14.404 165.312 2653 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.40 % Allowed : 8.23 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.19), residues: 1950 helix: 0.68 (0.16), residues: 1070 sheet: 0.08 (0.30), residues: 271 loop : 0.04 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 160 TYR 0.021 0.001 TYR C 124 PHE 0.008 0.001 PHE C 152 HIS 0.007 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (16607) covalent geometry : angle 0.54496 / 0.29 (22614) hydrogen bonds : bond 0.05130 / 3.41 ( 793) hydrogen bonds : angle 4.75765 / 3.34 ( 2241) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8339 (m-40) cc_final: 0.7783 (m-40) REVERT: A 222 ARG cc_start: 0.8294 (ttp-170) cc_final: 0.7944 (ttm170) REVERT: A 286 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7568 (m110) REVERT: A 309 MET cc_start: 0.8252 (ttm) cc_final: 0.7980 (ttp) REVERT: C 147 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7526 (mp) REVERT: C 178 MET cc_start: 0.9247 (mmt) cc_final: 0.8728 (mmt) REVERT: E 81 LYS cc_start: 0.8511 (mttt) cc_final: 0.7813 (tptt) REVERT: E 272 MET cc_start: 0.8142 (mtt) cc_final: 0.7926 (mtt) REVERT: E 330 THR cc_start: 0.8155 (m) cc_final: 0.7862 (p) REVERT: F 252 ASP cc_start: 0.7935 (m-30) cc_final: 0.7287 (p0) REVERT: F 296 ASP cc_start: 0.7664 (m-30) cc_final: 0.7398 (m-30) REVERT: H 200 ARG cc_start: 0.8126 (ttt180) cc_final: 0.7633 (mtp-110) outliers start: 23 outliers final: 15 residues processed: 257 average time/residue: 0.3160 time to fit residues: 117.1059 Evaluate side-chains 257 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 97 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 185 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 86 optimal weight: 0.2980 chunk 81 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.099035 restraints weight = 66834.152| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.17 r_work: 0.3007 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16607 Z= 0.118 Angle : 0.520 6.288 22614 Z= 0.272 Chirality : 0.040 0.128 2548 Planarity : 0.004 0.044 2808 Dihedral : 14.333 166.579 2653 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.10 % Allowed : 8.78 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 1950 helix: 0.84 (0.16), residues: 1072 sheet: 0.12 (0.30), residues: 271 loop : 0.11 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 160 TYR 0.019 0.001 TYR C 124 PHE 0.007 0.001 PHE A 58 HIS 0.007 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (16607) covalent geometry : angle 0.52018 / 0.27 (22614) hydrogen bonds : bond 0.04626 / 3.08 ( 793) hydrogen bonds : angle 4.62778 / 3.24 ( 2241) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 242 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8306 (m-40) cc_final: 0.7756 (m-40) REVERT: A 222 ARG cc_start: 0.8280 (ttp-170) cc_final: 0.7935 (ttm170) REVERT: A 286 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7536 (m110) REVERT: A 309 MET cc_start: 0.8232 (ttm) cc_final: 0.7956 (ttp) REVERT: C 90 LYS cc_start: 0.8230 (pttt) cc_final: 0.7973 (mtmm) REVERT: C 147 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7509 (mp) REVERT: C 178 MET cc_start: 0.9227 (mmt) cc_final: 0.8813 (mmt) REVERT: D 135 MET cc_start: 0.7777 (mmt) cc_final: 0.7505 (mmt) REVERT: E 81 LYS cc_start: 0.8499 (mttt) cc_final: 0.7786 (tptt) REVERT: E 272 MET cc_start: 0.8108 (mtt) cc_final: 0.7888 (mtt) REVERT: E 330 THR cc_start: 0.8155 (m) cc_final: 0.7860 (p) REVERT: H 200 ARG cc_start: 0.8089 (ttt180) cc_final: 0.7612 (mtp-110) outliers start: 18 outliers final: 11 residues processed: 248 average time/residue: 0.3188 time to fit residues: 113.1250 Evaluate side-chains 253 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 240 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 166 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 ASN ** H 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.098023 restraints weight = 67115.734| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.16 r_work: 0.2990 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16607 Z= 0.194 Angle : 0.560 6.304 22614 Z= 0.293 Chirality : 0.041 0.133 2548 Planarity : 0.005 0.047 2808 Dihedral : 14.368 160.429 2653 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.22 % Allowed : 8.90 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.19), residues: 1950 helix: 0.77 (0.16), residues: 1071 sheet: 0.20 (0.30), residues: 281 loop : -0.04 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 160 TYR 0.022 0.001 TYR C 124 PHE 0.010 0.001 PHE C 152 HIS 0.007 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (16607) covalent geometry : angle 0.55980 / 0.29 (22614) hydrogen bonds : bond 0.05250 / 3.49 ( 793) hydrogen bonds : angle 4.67800 / 3.29 ( 2241) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 245 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8319 (m-40) cc_final: 0.7782 (m-40) REVERT: A 222 ARG cc_start: 0.8320 (ttp-170) cc_final: 0.7962 (ttm170) REVERT: A 286 ASN cc_start: 0.7848 (OUTLIER) cc_final: 0.7593 (m110) REVERT: A 309 MET cc_start: 0.8288 (ttm) cc_final: 0.8000 (ttp) REVERT: C 110 ASP cc_start: 0.8679 (t0) cc_final: 0.8398 (m-30) REVERT: C 147 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7532 (mp) REVERT: C 178 MET cc_start: 0.9234 (mmt) cc_final: 0.8760 (mmt) REVERT: D 135 MET cc_start: 0.7867 (mmt) cc_final: 0.7609 (mmt) REVERT: E 81 LYS cc_start: 0.8553 (mttt) cc_final: 0.7766 (tptt) REVERT: E 105 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: E 272 MET cc_start: 0.8143 (mtt) cc_final: 0.7922 (mtt) REVERT: E 330 THR cc_start: 0.8169 (m) cc_final: 0.7881 (p) REVERT: F 252 ASP cc_start: 0.7919 (m-30) cc_final: 0.7303 (p0) REVERT: F 296 ASP cc_start: 0.7672 (m-30) cc_final: 0.7404 (m-30) REVERT: H 200 ARG cc_start: 0.8131 (ttt180) cc_final: 0.7638 (mtp-110) outliers start: 20 outliers final: 15 residues processed: 254 average time/residue: 0.3118 time to fit residues: 114.5789 Evaluate side-chains 257 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 239 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 175 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 107 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 ASN ** H 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.125789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.098790 restraints weight = 66200.962| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.14 r_work: 0.2921 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16607 Z= 0.119 Angle : 0.526 6.364 22614 Z= 0.275 Chirality : 0.040 0.129 2548 Planarity : 0.004 0.044 2808 Dihedral : 14.307 163.464 2653 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.04 % Allowed : 9.45 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 1950 helix: 0.94 (0.16), residues: 1072 sheet: 0.23 (0.30), residues: 281 loop : 0.11 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 160 TYR 0.018 0.001 TYR C 124 PHE 0.006 0.001 PHE A 58 HIS 0.006 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (16607) covalent geometry : angle 0.52614 / 0.27 (22614) hydrogen bonds : bond 0.04515 / 3.00 ( 793) hydrogen bonds : angle 4.53774 / 3.19 ( 2241) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 241 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8311 (m-40) cc_final: 0.7758 (m-40) REVERT: A 222 ARG cc_start: 0.8218 (ttp-170) cc_final: 0.7833 (ttm170) REVERT: A 286 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7493 (m110) REVERT: A 309 MET cc_start: 0.8210 (ttm) cc_final: 0.7887 (ttp) REVERT: B 105 ASP cc_start: 0.8901 (m-30) cc_final: 0.8615 (t0) REVERT: C 90 LYS cc_start: 0.8169 (pttt) cc_final: 0.7928 (mtmm) REVERT: C 147 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7381 (mp) REVERT: D 135 MET cc_start: 0.7804 (mmt) cc_final: 0.7544 (mmt) REVERT: E 81 LYS cc_start: 0.8403 (mttt) cc_final: 0.7601 (tptt) REVERT: E 105 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: E 117 MET cc_start: 0.7196 (tpp) cc_final: 0.6970 (tpt) REVERT: E 272 MET cc_start: 0.8133 (mtt) cc_final: 0.7911 (mtt) REVERT: E 330 THR cc_start: 0.8154 (m) cc_final: 0.7857 (p) outliers start: 17 outliers final: 11 residues processed: 246 average time/residue: 0.3130 time to fit residues: 111.2410 Evaluate side-chains 252 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 27 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 ASN ** H 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.126089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.099052 restraints weight = 66531.076| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.16 r_work: 0.3019 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16607 Z= 0.138 Angle : 0.529 6.202 22614 Z= 0.276 Chirality : 0.040 0.131 2548 Planarity : 0.005 0.044 2808 Dihedral : 14.285 162.410 2653 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.10 % Allowed : 9.63 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.19), residues: 1950 helix: 1.00 (0.16), residues: 1073 sheet: 0.19 (0.30), residues: 278 loop : 0.11 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 160 TYR 0.020 0.001 TYR C 124 PHE 0.007 0.001 PHE C 152 HIS 0.006 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (16607) covalent geometry : angle 0.52941 / 0.28 (22614) hydrogen bonds : bond 0.04545 / 3.02 ( 793) hydrogen bonds : angle 4.51584 / 3.17 ( 2241) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 242 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8291 (m-40) cc_final: 0.7748 (m-40) REVERT: A 222 ARG cc_start: 0.8313 (ttp-170) cc_final: 0.7947 (ttm170) REVERT: A 286 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7625 (m110) REVERT: A 309 MET cc_start: 0.8291 (ttm) cc_final: 0.8009 (ttp) REVERT: B 105 ASP cc_start: 0.8856 (m-30) cc_final: 0.8598 (t0) REVERT: C 90 LYS cc_start: 0.8247 (pttt) cc_final: 0.7983 (mtmm) REVERT: C 110 ASP cc_start: 0.8649 (t0) cc_final: 0.8363 (m-30) REVERT: C 147 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7573 (mp) REVERT: C 178 MET cc_start: 0.9246 (mmt) cc_final: 0.8836 (mmt) REVERT: D 39 LYS cc_start: 0.8171 (tttt) cc_final: 0.7854 (tptp) REVERT: D 135 MET cc_start: 0.7857 (mmt) cc_final: 0.7568 (mmt) REVERT: E 81 LYS cc_start: 0.8417 (mttt) cc_final: 0.7745 (tptt) REVERT: E 105 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7600 (m-30) REVERT: E 117 MET cc_start: 0.7322 (tpp) cc_final: 0.7104 (tpt) REVERT: E 272 MET cc_start: 0.8156 (mtt) cc_final: 0.7935 (mtt) REVERT: E 330 THR cc_start: 0.8117 (m) cc_final: 0.7829 (p) REVERT: F 296 ASP cc_start: 0.7625 (m-30) cc_final: 0.7343 (m-30) REVERT: H 200 ARG cc_start: 0.8063 (ttt180) cc_final: 0.7586 (mtp-110) outliers start: 18 outliers final: 13 residues processed: 248 average time/residue: 0.3141 time to fit residues: 111.5978 Evaluate side-chains 252 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 26 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 170 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.099302 restraints weight = 66229.661| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.15 r_work: 0.2987 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16607 Z= 0.130 Angle : 0.524 6.232 22614 Z= 0.272 Chirality : 0.040 0.130 2548 Planarity : 0.004 0.044 2808 Dihedral : 14.254 162.239 2653 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.98 % Allowed : 9.87 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1950 helix: 1.08 (0.16), residues: 1073 sheet: 0.19 (0.30), residues: 281 loop : 0.14 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 160 TYR 0.018 0.001 TYR C 124 PHE 0.006 0.001 PHE A 58 HIS 0.005 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (16607) covalent geometry : angle 0.52359 / 0.27 (22614) hydrogen bonds : bond 0.04416 / 2.93 ( 793) hydrogen bonds : angle 4.47510 / 3.14 ( 2241) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7694.04 seconds wall clock time: 130 minutes 47.01 seconds (7847.01 seconds total)